Real space refinement of complete virus structure
Dear all, I am trying to refine a complete virus pdb structure (possessing icosahedral symmetry) in a cryo-EM map using phenix.real_space_refine. The run fails complaining "Multi-model PDB (with MODEL-ENDMDL) is not supported". So, I followed a previous post in phenixbb: http://www.phenix-online.org/pipermail/phenixbb/2011-May/017079.html and merged multiple models into one but faced following problems: 1. This merged file is unreadable in UCSF Chimera. 2. The secondary structure definition in the PDB file header is not recognizable anymore in Phenix. In my understanding, both the problems are arising due to PDB format's inability to handle more than 62 chains and 99999 atoms in a file. So, what will be the work-around to perform a real space refinement of the complete virus structure at once? Also, how to maintain secondary structure during such refinement? Any help is highly appreciated. Best regards, Tofayel ............................................ Tofayel Ahmed Graduate Student (PhD) | Lab-02n-01 School of Biological Sciences Nanyang Technological University 60 Nanyang Drive, Singapore 637551 +65 8650.0473 |[email protected]mailto:[email protected]
Hi Tofayel,
I am trying to refine a complete virus pdb structure (possessing icosahedral symmetry) in a cryo-EM map using phenix.real_space_refine. The run fails complaining "Multi-model PDB (with MODEL-ENDMDL) is not supported". So, I followed a previous post in phenixbb: http://www.phenix-online.org/pipermail/phenixbb/2011-May/017079.html and merged multiple models into one
perhaps the advice you quote above is getting outdated a bit (though still valid!). Yes, most Phenix tools can't do much with multi-model files. In your case you can convert your multi-model file into a one model file where all the models become new chains. phenix.models_as_chains should do it for you.
but faced following problems:
1. This merged file is unreadable in UCSF Chimera.
I guess you better talk to Chimera developers unless it is clearly fault of Phenix.
2. The secondary structure definition in the PDB file header is not recognizable anymore in Phenix.
Please send us an example and we will investigate!
In my understanding, both the problems are arising due to PDB format's inability to handle more than 62 chains and 99999 atoms in a file.
With two-letter chain id and hybrid36 (both are used in Phenix) this is not the case, you can have way more chains and atoms. And if you go to mmCIF (which is the standard, and also supported in Phenix), then these limitations are nonexistent. Let us know if you have any questions or need help! Pavel
participants (2)
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#TOFAYEL AHMED#
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Pavel Afonine